Variant report

Variant	rs2704896
Chromosome Location	chr12:106649764-106649765
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:106640197..106643892-chr12:106649665..106652759,3	MCF-7	breast:
2	chr12:106645468..106647361-chr12:106648038..106649886,2	MCF-7	breast:
3	chr12:106649519..106651023-chr12:106669984..106671532,2	MCF-7	breast:
4	chr12:106647187..106649805-chr12:106683824..106686258,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000258355	Chromatin interaction
ENSG00000136026	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10507209	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[GIH][hapmap];0.85[LWK][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap]
rs1148413	0.91[ASW][hapmap];0.88[CEU][hapmap];0.82[GIH][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes]
rs1148415	0.88[CEU][hapmap];0.83[CHB][hapmap];0.85[AMR][1000 genomes]
rs1148417	0.84[CEU][hapmap];0.82[GIH][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1148419	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1148421	1.00[CEU][hapmap];0.93[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1148422	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1215740	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[GIH][hapmap];0.85[LWK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1215741	0.81[ASN][1000 genomes]
rs1215753	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1215757	0.87[EUR][1000 genomes]
rs1215759	0.87[EUR][1000 genomes]
rs1215761	0.91[ASW][hapmap];0.88[CEU][hapmap];0.82[GIH][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1215807	0.96[CEU][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12227822	0.87[ASN][1000 genomes]
rs12231439	0.87[ASN][1000 genomes]
rs12320181	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1237262	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[GIH][hapmap];0.85[LWK][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1238021	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2649705	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2649718	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2704895	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2704898	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2936701	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3741882	0.88[ASN][1000 genomes]
rs61942136	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1799917	chr12:106637876-106649988	Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	esv1834434	chr12:106637876-106649988	Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Strong transcription Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2704896	CCDC53	cis	cerebellum	SCAN
rs2704896	PRDM4	cis	cerebellum	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:106644200-106649800	Weak transcription	Fetal Heart	heart
2	chr12:106646200-106658800	Weak transcription	Monocytes-CD14+_RO01746	blood
3	chr12:106647800-106649800	Enhancers	H9 Cell Line	embryonic stem cell
4	chr12:106647800-106649800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr12:106649400-106650600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
6	chr12:106649600-106649800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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